Installation

HEMDAG is available on CRAN as well as through Bioconda and also from source code. You can use one of the following ways for installing HEMDAG.

Installation via Conda

Note

This is the recommended way of installing for normal users.

This is the recommended way to install HEMDAG because it will enables you to switch software versions easily. And in addition R with all needed dependencies will be installed.

First, you have to install the Miniconda Python3 distribution. See here for installation instructions. Make sure to …

  • Install the Python 3 version of Miniconda.
  • Answer yes to the question whether conda shall be put into your PATH.

Then, you can install HEMDAG with

$ conda install -c bioconda -c conda-forge r-hemdag

from the Bioconda channel.

Global Installation

You can directly install the library via R by issuing

$ R -e "install.packages('HEMDAG',repos = 'http://cran.us.r-project.org')"

in your terminal. But be sure to install R properly before that command.

Alternatively, you can install the HEMDAG library by typing in the R environment:

install.packages("HEMDAG");

Another possibility to install the development version of HEMDAG is by using the devtools package:

library(devtools);
install_github("marconotaro/HEMDAG");

Before running the above commands be sure to have correctly installed the devtools package (link)

Installing from Source

This section describes how to build HEMDAG from scratch.

Prequisites

For building HEMDAG, you will need the following dependencies

  • R (≥ 2.10)
  • R-libraries:
    • PerfMeas
    • rbgl (bioconductor)
    • graph (bioconductor)
    • precrec
    • preprocessCore (bioconductor)
    • plyr
    • foreach
    • doParallel

Package from CRAN

On a linux environment, download the package source from the CRAN repo and save it in the folder pippo. Then type:

R CMD INSTALL pippo/HEMDAG_2.6.0.tar.gz

Direct Git Checkout

Note

You only need to install from source if you want to develop HEMDAG yourself.

In this tutorial, we will download the HEMDAG sources and build them in ~/HEMDAG:

~ $ cd ~
~ $ git clone https://github.com/marconotaro/HEMDAG.git HEMDAG

Building

You can build HEMDAG by using:

R CMD build HEMDAG

This will generate the file HEMDAG_2.5.9.tar.gz and just install the package via:

R CMD INSTALL HEMDAG_2.5.9.tar.gz